I think it horses for courses, and there are both good and bad PCs and Indies. IMO it doesn't make a scrap of difference to the value if the stamps in the book of a 996 are from a PC or known Porsche specialist.
The thing about specialists is that they will do things that the PCs won't. Got a gasket leak on a 996 Tiptronic? The PC answer is an exchange transmission, whereas an indy will strip it and use the appropriate Mercedes/ZF gasket. Retrofit cruise? PC=no, Indy=yes. If the job isn't on the Porsche system, then a PC won't do it. I don't think it has anything to do with the technicians themselves, it is what Porsche AG decide. After all, most Indies were Porsche trained technicians in their time.
Then there is the parts issue. Indies source 'OEM' parts from different sources, whereas PCs are tied to Porsche. Original fitment items such as Bosch/Beru coil packs and Bosch MAF sensors considerably cheaper than PC prices, and the indy can pass that saving on to the customer, so it reduces the parts bill as well as the labour. Having said that, PCs can offer some keen fixed service pricing, but I suspect that it is because the indies are there, and the PCs are having to compete for work on the older models.